X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 298.0
Details The protein (about 5 mg/mL) was preincubated with the inhibitor (dissolved in dimethylsulfoxide) at a molar ratio of 1:5. Crystals were grown from 0.1 m sodium acetate buffer, pH 4.6 and 2M NaCl as precipitant. Crystals were cryo-cooled in liquid nitrogen after soaking in 30% glycerol to prevent freezing.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.57 α = 90
b = 86.52 β = 90
c = 46.32 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2017-06-28
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.5 50 96.8 0.059 -- -- 6.7 -- 37188 -- -- 17.7
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.5 1.55 76.4 0.493 -- 3.1 4.1 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.5 33.52 -- -- -- 35326 1818 96.75 -- 0.13356 0.13158 0.17132 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.501 1.54 -- 95 1953 0.188 0.248 -- 72.75
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.383
Anisotropic B[1][1] 0.48
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.43
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_other 2.597
r_mcangle_it 3.311
r_angle_other_deg 1.437
r_dihedral_angle_4_deg 8.495
r_gen_planes_other 0.002
r_scbond_other 4.573
r_scbond_it 4.598
r_bond_other_d 0.002
r_gen_planes_refined 0.011
r_angle_refined_deg 2.242
r_long_range_B_refined 4.742
r_bond_refined_d 0.019
r_mcbond_it 2.596
r_rigid_bond_restr 4.247
r_dihedral_angle_1_deg 7.001
r_chiral_restr 0.261
r_scangle_other 5.108
r_mcangle_other 3.316
r_long_range_B_other 4.743
r_dihedral_angle_2_deg 35.757
r_dihedral_angle_3_deg 13.536
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1514
Nucleic Acid Atoms 0
Heterogen Atoms 59
Solvent Atoms 133

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0238
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing version: 2.7.17